org.synbiohub.frontend

Class SynBioHubFrontend

java.lang.Object

org.synbiohub.frontend.SynBioHubFrontend

public class SynBioHubFrontend
extends Object

Provides a Java API to SynBioHub instances.

Author:

James McLaughlin, Chris Myers

Constructor Summary

Constructors

Constructor and Description
SynBioHubFrontend(String backendUrl) Creates an instance of the SynBioHub API.
SynBioHubFrontend(String backendUrl, int timeout) Creates an instance of the SynBioHub API.
SynBioHubFrontend(String backendUrl, String uriPrefix) Creates an instance of the SynBioHub API.
SynBioHubFrontend(String backendUrl, String uriPrefix, int timeout) Creates an instance of the SynBioHub API.

Method Summary

Modifier and Type	Method and Description
void	addToCollection(URI collectionUri, boolean overwrite, File file) Add file to an existing private collection on SynBioHub
void	addToCollection(URI collectionUri, boolean overwrite, InputStream inputStream) Add file to an existing private collection on SynBioHub
void	addToCollection(URI collectionUri, boolean overwrite, SBOLDocument document) Add SBOL document to an existing private collection on SynBioHub
void	addToCollection(URI collectionUri, boolean overwrite, String filename) Add file to an existing private collection on SynBioHub
void	attachFile(URI topLevelUri, File file) Attach a file to an object in SynBioHub.
void	attachFile(URI topLevelUri, InputStream inputStream) Attach a file to an object in SynBioHub.
void	attachFile(URI topLevelUri, InputStream inputStream, String filename) Attach a file to an object in SynBioHub.
void	attachFile(URI topLevelUri, String filename) Attach a file to an object in SynBioHub.
void	createCollection(String id, String version, String name, String description, String citations, boolean overwrite) Create a new private collection on SynBioHub
void	createCollection(String id, String version, String name, String description, String citations, boolean overwrite, File file) Create a new private collection on SynBioHub and add the contents of the file to this collection
void	createCollection(String id, String version, String name, String description, String citations, boolean overwrite, InputStream inputStream) Create a new private collection on SynBioHub and add the contents of the file to this collection
void	createCollection(String id, String version, String name, String description, String citations, boolean overwrite, SBOLDocument document) Create a new private collection on SynBioHub and add the contents of the SBOL document to this collection
void	createCollection(String id, String version, String name, String description, String citations, boolean overwrite, String filename) Create a new private collection on SynBioHub and add the contents of the file to this collection
String	getAttachment(URI attachmentUri, OutputStream outputStream) Retrieve an attachment from a SynBioHub instance using its URI, and save into the provided output stream.
String	getAttachment(URI attachmentUri, String path) Retrieve an attachment from a SynBioHub instance using its URI, and save to the path provided.
String	getBackendUrl() Returns the URL for the SynBioHub instance.
int	getCount(String objectType) Return the total number of objects of a specified type in the repository.
ArrayList<IdentifiedMetadata>	getMatchingComponentDefinitionMetadata(String name, Set<URI> roles, Set<URI> types, Set<URI> collections, Integer offset, Integer limit) Search the default store for ComponentDefinition instances matching a name and/or a set of roles
static ArrayList<WebOfRegistriesData>	getRegistries() Fetch data about all registries in the web of registries.
static ArrayList<WebOfRegistriesData>	getRegistries(String webOfRegistriesUrl) Fetch data about all registries in the web of registries.
ArrayList<IdentifiedMetadata>	getRootCollectionMetadata() Search the default store for Collections that are not members of any other Collections
SBOLDocument	getSBOL(URI topLevelUri) Retrieve SBOL TopLevel object from a SynBioHub instance using its URI.
SBOLDocument	getSBOL(URI topLevelUri, boolean recursive) Retrieve SBOL TopLevel object from a SynBioHub instance using its URI.
ArrayList<IdentifiedMetadata>	getSubCollectionMetadata(URI parentCollectionUri) Search the default store for Collections that are members of the specified Collection
String	getUsername() Returns the username of the logged in user
boolean	isSetUsername() Returns if a user is logged in
void	login(String email, String password) Login to the SynBioHub.
void	logout() Sets the user to null to indicate that no user is logged in.
void	removeRegistryParts(SBOLDocument document) Remove all parts from this registry from a given SBOL document
void	removeSBOL(URI topLevelUri) Remove SBOL TopLevel object from a SynBioHub instance using its URI.
void	replaceSBOL(URI topLevelUri) Remove SBOL TopLevel object from a SynBioHub instance using its URI, but leave references to this object, since it is going to be replaced.
ArrayList<IdentifiedMetadata>	search(SearchQuery query) Search this SynBioHub instance for objects matching a search query
String	sparqlQuery(String query) Perform a SPARQL query

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SynBioHubFrontend

public SynBioHubFrontend(String backendUrl,
                         String uriPrefix)

Creates an instance of the SynBioHub API.

Parameters:

backendUrl - - URL for the SynBioHub instance.

uriPrefix - - prefix for all URIs stored in this repository

SynBioHubFrontend

public SynBioHubFrontend(String backendUrl)

Creates an instance of the SynBioHub API.

Parameters:

backendUrl - - URL for the SynBioHub instance.

SynBioHubFrontend

public SynBioHubFrontend(String backendUrl,
                         int timeout)

Creates an instance of the SynBioHub API.

Parameters:

backendUrl - - URL for the SynBioHub instance.

timeout - - timeout for connections in seconds

SynBioHubFrontend

public SynBioHubFrontend(String backendUrl,
                         String uriPrefix,
                         int timeout)

Creates an instance of the SynBioHub API.

Parameters:

backendUrl - - URL for the SynBioHub instance.

uriPrefix - - prefix for all URIs stored in this repository

timeout - - timeout for connections in seconds

Method Detail

getBackendUrl

public String getBackendUrl()

Returns the URL for the SynBioHub instance.

Returns:

the URL for the SynBioHub instance.

getCount

public int getCount(String objectType)
             throws SynBioHubException

Return the total number of objects of a specified type in the repository.

Parameters:

objectType - The object type to count (Collection, ComponentDefinition, Sequence, ModuleDefinition, Model, etc.).

Returns:

the total number of objects of a specified type in the repository.

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

getSBOL

public SBOLDocument getSBOL(URI topLevelUri)
                     throws SynBioHubException

Retrieve SBOL TopLevel object from a SynBioHub instance using its URI.

Parameters:

topLevelUri - The URI of the SBOL TopLevel

Returns:

A libSBOLj TopLevel instance corresponding to the TopLevel

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

getSBOL

public SBOLDocument getSBOL(URI topLevelUri,
                            boolean recursive)
                     throws SynBioHubException

Retrieve SBOL TopLevel object from a SynBioHub instance using its URI.

Parameters:

topLevelUri - The URI of the SBOL TopLevel

recursive - indicates if the complete SBOL document should be fetched recursively

Returns:

A libSBOLj TopLevel instance corresponding to the TopLevel

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

getAttachment

public String getAttachment(URI attachmentUri,
                            String path)
                     throws SynBioHubException,
                            IOException

Retrieve an attachment from a SynBioHub instance using its URI, and save to the path provided.

Parameters:

attachmentUri - The URI of the SBOL Attachment object

path - The path to store the downloaded attachment

Returns:

the name of the file being downloaded

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

IOException - if there is an I/O error

getAttachment

public String getAttachment(URI attachmentUri,
                            OutputStream outputStream)
                     throws SynBioHubException,
                            IOException

Retrieve an attachment from a SynBioHub instance using its URI, and save into the provided output stream.

Parameters:

attachmentUri - The URI of the SBOL Attachment object

outputStream - The output stream to store the downloaded attachment

Returns:

the name of the file being downloaded

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

IOException - if there is an I/O error

removeSBOL

public void removeSBOL(URI topLevelUri)
                throws SynBioHubException

Remove SBOL TopLevel object from a SynBioHub instance using its URI.

Parameters:

topLevelUri - The URI of the SBOL TopLevel

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

replaceSBOL

public void replaceSBOL(URI topLevelUri)
                 throws SynBioHubException

Remove SBOL TopLevel object from a SynBioHub instance using its URI, but leave references to this object, since it is going to be replaced.

Parameters:

topLevelUri - The URI of the SBOL TopLevel

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

getMatchingComponentDefinitionMetadata

public ArrayList<IdentifiedMetadata> getMatchingComponentDefinitionMetadata(String name,
                                                                            Set<URI> roles,
                                                                            Set<URI> types,
                                                                            Set<URI> collections,
                                                                            Integer offset,
                                                                            Integer limit)
                                                                     throws SynBioHubException

Search the default store for ComponentDefinition instances matching a name and/or a set of roles

Parameters:

name - The dcterms:title to search for, or null

roles - A set of role URIs to search for, or null

types - A set of type URIs to search for, or null

collections - A set of Collection URIs to search for, or null

offset - The offset of the results to begin at, or null to begin at 0

limit - The maximum number of results to return, or null to return all results

Returns:

An ArrayList of ComponentDefinitionMetaData objects with a summary of all matching ComponentDefinitions.

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

search

public ArrayList<IdentifiedMetadata> search(SearchQuery query)
                                     throws SynBioHubException

Search this SynBioHub instance for objects matching a search query

Parameters:

query - the search query

Returns:

An ArrayList of MetaData for objects that match the specified search query

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

getRootCollectionMetadata

public ArrayList<IdentifiedMetadata> getRootCollectionMetadata()
                                                        throws SynBioHubException

Search the default store for Collections that are not members of any other Collections

Returns:

An ArrayList of CollectionMetaData objects with a summary of all matching Collections.

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

getRegistries

public static ArrayList<WebOfRegistriesData> getRegistries()
                                                    throws SynBioHubException

Fetch data about all registries in the web of registries.

Returns:

An ArrayList of WebOfRegistriesData describing each registry in the web of registries.

Throws:

SynBioHubException - if there was an error communicating with the WebOfRegistries

getRegistries

public static ArrayList<WebOfRegistriesData> getRegistries(String webOfRegistriesUrl)
                                                    throws SynBioHubException

Fetch data about all registries in the web of registries.

Parameters:

webOfRegistriesUrl - The URL for the web-of-registries.

Returns:

An ArrayList of WebOfRegistriesData describing each registry in the web of registries.

Throws:

SynBioHubException - if there was an error communicating with the web-of-registries

sparqlQuery

public String sparqlQuery(String query)
                   throws SynBioHubException

Perform a SPARQL query

Parameters:

query - SPARQL query string

Returns:

result as a JSON string

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

getSubCollectionMetadata

public ArrayList<IdentifiedMetadata> getSubCollectionMetadata(URI parentCollectionUri)
                                                       throws SynBioHubException

Search the default store for Collections that are members of the specified Collection

Parameters:

parentCollectionUri - URI for Collection to search for member Collections

Returns:

An ArrayList of CollectionMetaData objects with a summary of all matching Collections.

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

logout

public void logout()

Sets the user to null to indicate that no user is logged in.

isSetUsername

public boolean isSetUsername()

Returns if a user is logged in

Returns:

true if a user is logged in

getUsername

public String getUsername()

Returns the username of the logged in user

Returns:

the username of the logged in user

login

public void login(String email,
                  String password)
           throws SynBioHubException

Login to the SynBioHub.

Parameters:

email - The user's email

password - The user's password

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

removeRegistryParts

public void removeRegistryParts(SBOLDocument document)

Remove all parts from this registry from a given SBOL document

Parameters:

document - The document to remove all registry parts from

attachFile

public void attachFile(URI topLevelUri,
                       String filename)
                throws SynBioHubException,
                       FileNotFoundException

Attach a file to an object in SynBioHub.

Parameters:

topLevelUri - identity of the object to attach the file to

filename - the name of the file to attach

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

FileNotFoundException - if the file is not found

attachFile

public void attachFile(URI topLevelUri,
                       File file)
                throws SynBioHubException,
                       FileNotFoundException

Attach a file to an object in SynBioHub.

Parameters:

topLevelUri - identity of the object to attach the file to

file - the file to attach

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

FileNotFoundException - if the file is not found

attachFile

public void attachFile(URI topLevelUri,
                       InputStream inputStream)
                throws SynBioHubException

Attach a file to an object in SynBioHub.

Parameters:

topLevelUri - identity of the object to attach the file to

inputStream - the inputStream to attach

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

attachFile

public void attachFile(URI topLevelUri,
                       InputStream inputStream,
                       String filename)
                throws SynBioHubException

Attach a file to an object in SynBioHub.

Parameters:

topLevelUri - identity of the object to attach the file to

inputStream - the inputStream to attach

filename - name of file to attach

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

addToCollection

public void addToCollection(URI collectionUri,
                            boolean overwrite,
                            SBOLDocument document)
                     throws SynBioHubException

Add SBOL document to an existing private collection on SynBioHub

Parameters:

collectionUri - Identity of the private collection

overwrite - if object exists in collection, overwrite it

document - the SBOL document to submit

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

addToCollection

public void addToCollection(URI collectionUri,
                            boolean overwrite,
                            String filename)
                     throws SynBioHubException,
                            IOException

Add file to an existing private collection on SynBioHub

Parameters:

collectionUri - Identity of the private collection

overwrite - if object exists in collection, overwrite it

filename - filename to submit to SynBioHub

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

IOException - if there is an I/O error

addToCollection

public void addToCollection(URI collectionUri,
                            boolean overwrite,
                            File file)
                     throws SynBioHubException,
                            IOException

Add file to an existing private collection on SynBioHub

Parameters:

collectionUri - Identity of the private collection

overwrite - if object exists in collection, overwrite it

file - file to submit to SynBioHub

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

IOException - if there is an I/O error

addToCollection

public void addToCollection(URI collectionUri,
                            boolean overwrite,
                            InputStream inputStream)
                     throws SynBioHubException

Add file to an existing private collection on SynBioHub

Parameters:

collectionUri - Identity of the private collection

overwrite - if object exists in collection, overwrite it

inputStream - inputStream to submit to SynBioHub

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

createCollection

public void createCollection(String id,
                             String version,
                             String name,
                             String description,
                             String citations,
                             boolean overwrite)
                      throws SynBioHubException

Create a new private collection on SynBioHub

Parameters:

id - The submission identifier

version - The submission version

name - The submission name

description - The submission description

citations - The pubMedIds for this submission

overwrite - if collection exists, overwrite it

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

createCollection

public void createCollection(String id,
                             String version,
                             String name,
                             String description,
                             String citations,
                             boolean overwrite,
                             SBOLDocument document)
                      throws SynBioHubException

Create a new private collection on SynBioHub and add the contents of the SBOL document to this collection

Parameters:

id - The submission identifier

version - The submission version

name - The submission name

description - The submission description

citations - The pubMedIds for this submission

overwrite - if collection exists, overwrite it

document - the SBOL document to submit

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

createCollection

public void createCollection(String id,
                             String version,
                             String name,
                             String description,
                             String citations,
                             boolean overwrite,
                             String filename)
                      throws SynBioHubException,
                             IOException

Create a new private collection on SynBioHub and add the contents of the file to this collection

Parameters:

id - The submission identifier

version - The submission version

name - The submission name

description - The submission description

citations - The pubMedIds for this submission

overwrite - if collection exists, overwrite it

filename - filename to submit to SynBioHub

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

IOException - if there is an I/O error

createCollection

public void createCollection(String id,
                             String version,
                             String name,
                             String description,
                             String citations,
                             boolean overwrite,
                             File file)
                      throws SynBioHubException,
                             IOException

Create a new private collection on SynBioHub and add the contents of the file to this collection

Parameters:

id - The submission identifier

version - The submission version

name - The submission name

description - The submission description

citations - The pubMedIds for this submission

overwrite - if collection exists, overwrite it

file - file to submit to SynBioHub

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub

IOException - if there is an I/O error

createCollection

public void createCollection(String id,
                             String version,
                             String name,
                             String description,
                             String citations,
                             boolean overwrite,
                             InputStream inputStream)
                      throws SynBioHubException

Create a new private collection on SynBioHub and add the contents of the file to this collection

Parameters:

id - The submission identifier

version - The submission version

name - The submission name

description - The submission description

citations - The pubMedIds for this submission

overwrite - if collection exists, overwrite it

inputStream - inputStream to submit to SynBioHub

Throws:

SynBioHubException - if there was an error communicating with the SynBioHub